Mercurial > repos > iuc > trinity_abundance_estimates_to_matrix

annotate abundance_estimates_to_matrix.xml @ 17:2e21a7c28b38 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
author iuc
date Fri, 10 Sep 2021 22:51:58 +0000
parents 0f445c315a08
children 442e3696c634
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1 <tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@">
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2 <description>for a de novo assembly of RNA-Seq data by Trinity</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
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9 <requirement type="package" version="0.44.0">kallisto</requirement>
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10 </expand>
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11 <command detect_errors="aggressive"><![CDATA[
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12 #import re
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13 #for $entry in $samples:
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14 ln -f -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' &&
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15 #end for
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17 abundance_estimates_to_matrix.pl
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19 --est_method ${est_method}
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20 --cross_sample_norm ${additional_params.cross_sample_norm}
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21
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22 #if $gene_trans_map:
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23 --gene_trans_map '$gene_trans_map'
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24 #else:
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25 --gene_trans_map 'none'
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26 #end if
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27
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28 #for $entry in $samples:
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29 '${re.sub('[^\w\-_]', '_', entry.element_identifier)}'
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30 #end for
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32 && mv *.isoform.counts.matrix '$trans_counts'
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33 && mv *.isoform.TPM.not_cross_norm '$TPM_no_norm'
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34 #if $gene_trans_map:
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35 && mv *.gene.counts.matrix '$trans_counts_gene'
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36 && mv *.gene.TPM.not_cross_norm '$TPM_no_norm_gene'
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37 #end if
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39 #if $additional_params.cross_sample_norm == "TMM":
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40 && mv *.isoform.TMM.EXPR.matrix '$norm_TMM'
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41 #if $gene_trans_map:
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42 && mv *.gene.TMM.EXPR.matrix '$norm_TMM_gene'
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43 #end if
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44 #else if $additional_params.cross_sample_norm == "UpperQuartile":
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45 && mv *.isoform.UpperQuartile.EXPR.matrix '$norm_UQ'
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46 #if $gene_trans_map:
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47 && mv *.gene.UpperQuartile.EXPR.matrix '$norm_UQ_gene'
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48 #end if
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49 #end if
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50 ]]></command>
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51 <inputs>
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52 <param name="samples" label="Abundance estimates" type="data" multiple="true" format="tabular" help="output(s) from 'Align reads and estimate abundance' tool" />
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53 <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" optional="true" help="Only needed for gene level estimates" />
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54 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
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55 <option value="RSEM">RSEM</option>
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56 <option value="eXpress">eXpress</option>
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57 <option value="salmon">Salmon</option>
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58 <option value="kallisto">Kallisto</option>
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59 </param>
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61 <section name="additional_params" title="Additional Options" expanded="False">
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62 <param type="select" name="cross_sample_norm" argument="--cross_sample_norm" label="Cross sample normalization">
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63 <option value="TMM">TMM</option>
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64 <option value="UpperQuartile">UpperQuartile</option>
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65 <option value="none">None</option>
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66 </param>
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67 </section>
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68 </inputs>
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69 <outputs>
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70 <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment isoform counts (raw counts)"/>
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71 <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of isoform TPM expression values (not cross-sample normalized)"/>
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73 <data format="tabular" name="trans_counts_gene" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment gene counts (raw counts)">
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74 <filter>gene_trans_map</filter>
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75 </data>
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76 <data format="tabular" name="TPM_no_norm_gene" label="${tool.name} on ${on_string}: matrix of gene TPM expression values (not cross-sample normalized)">
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77 <filter>gene_trans_map</filter>
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78 </data>
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80 <data format="tabular" name="norm_TMM" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values">
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81 <filter>additional_params['cross_sample_norm'] == "TMM"</filter>
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82 </data>
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83 <data format="tabular" name="norm_UQ" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values">
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84 <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter>
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85 </data>
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87 <data format="tabular" name="norm_TMM_gene" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values">
13ab393ba794 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 7
diff changeset
88 <filter>additional_params['cross_sample_norm'] == "TMM" and gene_trans_map</filter>
13ab393ba794 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 7
diff changeset
89 </data>
13ab393ba794 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 7
diff changeset
90 <data format="tabular" name="norm_UQ_gene" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values">
13ab393ba794 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 7
diff changeset
91 <filter>additional_params['cross_sample_norm'] == "UpperQuartile" and gene_trans_map</filter>
13ab393ba794 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 7
diff changeset
92 </data>
0
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
93 </outputs>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
94 <tests>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
95 <test>
1
fba77b1f69b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents: 0
diff changeset
96 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/>
0
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
97 <param name="est_method" value="RSEM"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
98 <param name="cross_sample_norm" value="TMM"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
99 <output name="trans_counts">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
100 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
101 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
102 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
103 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
104 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
105 <output name="TPM_no_norm">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
106 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
107 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
108 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
109 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
110 </output>
10
13ab393ba794 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 7
diff changeset
111 <output name="norm_TMM">
0
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
112 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
113 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
114 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
115 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
116 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
117 </test>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
118 <test>
1
fba77b1f69b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents: 0
diff changeset
119 <param name="samples" ftype="tabular" value="count/rsem_bowtie2/sample_A,count/rsem_bowtie2/sample_B"/>
0
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
120 <param name="est_method" value="RSEM"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
121 <param name="cross_sample_norm" value="TMM"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
122 <output name="trans_counts">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
123 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
124 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
125 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
126 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
127 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
128 <output name="TPM_no_norm">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
129 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
130 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
131 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
132 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
133 </output>
10
13ab393ba794 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 7
diff changeset
134 <output name="norm_TMM">
0
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
135 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
136 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
137 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
138 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
139 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
140 </test>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
141 <test>
1
fba77b1f69b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents: 0
diff changeset
142 <param name="samples" ftype="tabular" value="count/express_bowtie/sample_A,count/express_bowtie/sample_B"/>
0
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
143 <param name="est_method" value="eXpress"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
144 <param name="cross_sample_norm" value="TMM"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
145 <output name="trans_counts">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
146 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
147 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
148 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
149 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
150 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
151 <output name="TPM_no_norm">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
152 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
153 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
154 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
155 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
156 </output>
10
13ab393ba794 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 7
diff changeset
157 <output name="norm_TMM">
0
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
158 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
159 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
160 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
161 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
162 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
163 </test>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
164 <test>
1
fba77b1f69b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents: 0
diff changeset
165 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/>
0
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
166 <param name="est_method" value="RSEM"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
167 <param name="cross_sample_norm" value="UpperQuartile"/>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
168 <output name="trans_counts">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
169 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
170 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
171 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
172 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
173 </output>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
174 <output name="TPM_no_norm">
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
175 <assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
176 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
177 <has_n_columns n="3" />
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
178 </assert_contents>
77fc547df6ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
179 </output>
10
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180 <output name="norm_UQ">
0
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181 <assert_contents>
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182 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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183 </assert_contents>
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184 </output>
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185 </test>
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186 <test>
1
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187 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/>
0
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188 <param name="est_method" value="RSEM"/>
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189 <param name="cross_sample_norm" value="none"/>
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190 <output name="trans_counts">
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191 <assert_contents>
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192 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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193 <has_n_columns n="3" />
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194 </assert_contents>
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195 </output>
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196 <output name="TPM_no_norm">
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197 <assert_contents>
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198 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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199 <has_n_columns n="3" />
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200 </assert_contents>
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201 </output>
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202 </test>
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203 <test>
1
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204 <param name="samples" ftype="tabular" value="count/salmon/sample_A,count/salmon/sample_B"/>
0
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205 <param name="est_method" value="salmon"/>
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206 <param name="cross_sample_norm" value="none"/>
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207 <output name="trans_counts">
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208 <assert_contents>
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209 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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210 <has_n_columns n="3" />
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211 </assert_contents>
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212 </output>
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213 <output name="TPM_no_norm">
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214 <assert_contents>
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215 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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216 <has_n_columns n="3" />
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217 </assert_contents>
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218 </output>
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219 </test>
6
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220 <test>
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221 <param name="samples" ftype="tabular" value="count/kallisto/abundance.tsv.genes,count/kallisto/abundance_B.tsv.genes"/>
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222 <param name="est_method" value="kallisto"/>
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223 <param name="cross_sample_norm" value="TMM"/>
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224 <output name="trans_counts">
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225 <assert_contents>
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226 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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227 <has_n_columns n="3" />
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228 </assert_contents>
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229 </output>
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230 <output name="TPM_no_norm">
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231 <assert_contents>
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diff changeset
232 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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iuc
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233 <has_n_columns n="3" />
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234 </assert_contents>
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235 </output>
10
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236 <output name="norm_TMM">
6
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237 <assert_contents>
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238 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
74217fbfba4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
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239 <has_n_columns n="3" />
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240 </assert_contents>
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241 </output>
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242 </test>
0
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243 </tests>
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244 <help>
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245 <![CDATA[
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246 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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247 This tool will combine abundance estimations (produced by 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool) from multiple samples into a single tabular file.
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248 This matrix can then be used by 'RNASeq samples quality check for transcript quantification' and 'Differential Expression Analysis using a Trinity assembly' tools.
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249
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250 **Inputs**
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251
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252 It takes as input multiple results from 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool/
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253 Each sample must have a name, that should be used in subsequent tools.
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254
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255 **Output**
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256
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257 This tool will produce a single matrix file. More details on this page:
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258
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259 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification
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260
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261
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262 .. _Trinity: http://trinityrnaseq.github.io
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263 ]]>
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264 </help>
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265
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266 <expand macro="citation" />
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267 </tool>